rMATS BAM file MemoryError Issue

Question

[saipra003]

Hi everyone! This is my first time posting here. I have a very large BAM file (4.8GB) which I would like to process using the rMATS program to find splice variants. However, when I pass in the file through rMATS, I am receiving the following error.

Some searching online revealed that the BAM file might be too big to process through the rMATS pipeline. I tried to split the BAM file by chromosome, but I end up getting many different files (I've also included a partial list of the chromosomes below).

Could someone please recommend a way for me to split the BAM file in a different manner? Thanks in advance!

[Pierre Lindenbaum]

what was your command line ?

[saipra003]

Hi, The command line input that generated the error was: rmats.py --b1 <path to .bam file> --gtf <path to .gtf file> -t paired --readLength 61 --variable-read-length --nthread 4 --od <path to output directory> --tmp <path to temporary output directory>

The second image was generated using the following command: bamtools header -in <input file>.bam

[GenoMax]

Some searching online revealed that the BAM file might be too big to process through the rMATS pipeline

Where is the reference for this?

Since you are providing a temporary directory to the program it should be able to handle this BAM file (speculation). Looks like you are likely running out of RAM. How much RAM do you have?

[saipra003]

Hi GenoMax, Please look at Pierre Lindenbaum's response below. Instead of passing a .txt file with pathways to the .bam files, I was passing in the .bam files themselves causing rMATS to throw a memory error.

Answer 1

[Pierre Lindenbaum]

The command line input that generated the error was: rmats.py --b1 <path to .bam file> --gtf <path to .gtf file> -t paired --readLength 61 --variable-read-length --nthread 4 --od <path to output directory> --tmp <path to temporary output directory>

https://github.com/Xinglab/rmats-turbo#all-arguments

--b1 B1               A text file containing a comma separated list of the
                        BAM files for sample_1. (Only if using BAM)

as specified in the manual --b1 is NOT a path to the bam file.

[saipra003]

Thank you so much!